Scott Fappiano didn’t know it for most of his 21 years behind bars, but his fate rested inside two test tubes.

The fragile vials, orphaned from an unsuccessful 1989 DNA test, were jostled by dozens of people, trucked hundreds of miles across the Northeast and banished to a succession of storage vaults.

Somehow they survived, without shattering, without spilling. And, incredibly, they were found.

While their trail illuminates how government can lose track of the smallest biological crime relics, it also shows how private labs often safeguard the lowliest of specimens.

“We got Scott out of prison, but it was a cruel cosmic joke in the meantime,” said his lawyer Nina Morrison of the Innocence Project, who spent two years hunting down Fappiano’s lost evidence.

The odyssey dates to the December 1983 rape of a police officer’s wife.

Shortly after midnight, a gun-wielding intruder crept through the window of the couple’s Brooklyn apartment. Once in, he tied the officer to the couple’s bedpost, raped the officer’s wife repeatedly, smoked a cigarette and downed a couple of beers.

Among the many pieces of evidence he left behind were the future contents of the test tubes – his semen on her white sweat pants.

Soon after, the victim picked Fappiano from a batch of police photos. The 22-year- old Brooklyn native had a juvenile offense, had features similar to the attacker’s and lived just blocks from her apartment.

Authorities had all they needed for a conviction after her husband also pointed to him during a physical lineup.

Fappiano was sent away for 50 years.

“Don’t forget about me,” he told his girlfriend, Joanne.

Driven to be cleared

Fappiano decided he wouldn’t be a slave to prison time. Unlike other prisoners, he wouldn’t mark off calendar pages. He wouldn’t stay up late watching TV. Instead, his reality became immersion in a legal bid for the freedom he knew he deserved.

By 1989, time was an ally for him in one respect: DNA testing had dawned. Fappiano learned he could apply genetic fingerprinting to the evidence in his case. But he couldn’t track any of the exhibits except for the stained sweat pants. The district attorney agreed to DNA testing, shipping the pants to Lifecodes Corp., then one of the biggest forensic labs in the country.

An analyst there cut out the stains and submerged them in test tubes to separate the DNA from the fabric. But there wasn’t enough semen to yield readable results. “No comparisons could be made,” the lab reported.

The news floored Fappiano, who said he couldn’t help but wonder whether other lost evidence, such as the rape evidence kit, contained enough semen to test.

Back at the lab in Elmhurst, N.Y., leftovers from the testing – two plastic tubes containing a brownish liquid – remained. But New York state law doesn’t regulate the handling of leftover extracts, let alone original DNA specimens.

The private Lifecodes, however, did. Its policies called for preserving the tubes indefinitely.

So lab workers labeled them and placed them upright like lipsticks in a cold vault with hundreds of other specimens at minus 80 degrees Celsius.

The tubes stayed in the freezer at the same temperature until 1992. That’s when Lifecodes finalized a deal to break from its parent corporation and move to Stamford, Conn.

As with most corporate moves, workers swept stuff into the garbage bin to make the relocation easier. But they kept the vault specimens, as policy dictated. They placed the tubes into a picnic-style Styrofoam chest packed with dry ice and loaded it into the back of a Ryder truck. From there, the tubes bumped their way, 40 miles, to Stamford.

Fappiano, meanwhile, endured his own bumpy journey, shuffled to nine different prisons, sometimes for breaking the rules, such as refusing to join a sex-offender counseling program.

Company changed, policy didn’t

Back in Stamford, the tubes sat in a fridge inside an 8-by-11-foot storage room about the size of Fappiano’s cell. Over the years, the shelves around them sagged with hundreds of other forgotten vials, afterthoughts from other DNA tests performed by the company’s analysts.

Having separated from its parent company, Lifecodes bought another lab, Cellmark Diagnostics. Those labs then got bought by a bigger company, which changed their name to Orchid BioScience, which then underwent another name change to Orchid Cellmark Inc.

Back at prison, he fired off letters in hopes of finding evidence for advanced DNA tests.

In 2002, he hooked the interest of lawyer Morrison.

For two years, she and her law-student assistant Lauren Yates peppered law-enforcement agencies with requests to search, only to discover everything in Fappiano’s case gone.

Back in Stamford, the tubes’ future was precarious. Tepnel Life Sciences had bought the Lifecodes diagnostics division and its Stamford facility holding the tubes. It had no use for forensic specimens.

But before throwing them out, a Stamford scientist phoned Mark Stolorow, Orchid-Cellmark’s new forensic chief, who extended Lifecode’s preservation policy.

“We’ll send a truck for them,” he said.

The tubes were removed from the freezer and then hauled 278 miles to Orchid- Cellmark’s DNA lab in Germantown, Md.

At the Innocence Project offices, Morrison learned in November 2004 that the DA’s efforts to locate evidence, at her behest, had hit a dead end.

But soon, she also learned from Stolorow that Orchid had inherited a large stash of old evidence specimens. She gave him the Lifecodes lab number originally assigned to Fappiano, who by then had done 20 years behind bars.

“Is there any way you can accelerate this?” she asked.

“I’ll do my best,” came the reply.

It would take months for Orchid’s workers to comb through the unlabeled boxes. Through January 2006, Morrison asked for updates. Then, through March, April, May and June.

By summer, she got the news she wanted. A couple of tiny translucent tubes with Fappiano’s label number had been found – still intact, unspilled and temperature-controlled.

And then one final road trip, in the back of a FedEx truck 244 miles to the New York City medical examiner’s office.

There they were uncapped for the first time in 17 years and tested using new technology. The result: The semen wasn’t Fappiano’s.

But additional rounds of tests were necessary to establish that the tubes had been labeled properly. They needed to verify that the victim’s DNA was also present and that the male DNA wasn’t her husband’s.

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